El Capitan slow reboot/shutdown

I upgraded to El Cap awhile back and was having issues so I cloned back Yosemite. I thought I would try it again and theres still issues. One being it's super slow on reboots and shutdowns. I have a 2012 Mac Mini with a SSD and 8GB of RAM.

I even partitioned my drive and just installed El Cap and it still takes up to a min to reboot and shutdown. Not a huge deal but I don't have any of these issues on Yosemite.

Like I said, theres a coupe more things going on but thought I would see if anyone had any idea whats going on. Maybe it's just normal?

Thanks

Has it finished the re-indexing of the drive for Spotlight? That process runs in the background and can take hours, sometimes days, to complete, particularly if you have a lot of stuff on the hard drive or a lot of external drives attached. Also, if you do have external drives, the OS has to unmount them before shutting down and the process can take a while, particularly if the re-index is holding the drive. You get into a bit of "after you, no after you" action as the shutdown tries to unmount, but the indexing says "hold on I'm busy" and keeps the drive active. Then the OS shifts to closing the application but indexing says "wait, I need to close the drive first." This ping-pings for a bit until one or the other reaches a stopping point.

Thanks for the reply. I really don't know if it has finished. I have Yosemite cloned back and like I said partitioned a small part of the drive to test some things out like Photoshop.

So boot up in the El Cap partition and let it sit for awhile and see if that helps?

Well, that's up to you. I was just suggestion one possible cause of slow start/shutdown.

How much space is available on the El Capitan partition? If there is not enough available room, that can cause slow behavior also.

My setup now is I have a 128 GB SSD with all applications on it and a 500GB HDD with the home folder on it. Thats the setup I had when I tried out El Cap months ago. So I upgraded to El Cap a few days ago to see if things were any better and all the issues were still there. So I partitioned 35GB of the SSD to do some trouble shooting. There's about 17GB of available space on the partition. But I had the same behavior when I had El Cap installed with plenty of space on the SSD and HDD.

I turned of indexing of the partition to see if that helped but it didn't seem to.

I found a thread where a someone was having the same issue and a Apple support rep recommend deleting a couple of user agent files. I did that and it rebooted normally on the first try but went back to the same behavior after trying another reboot.

Again, it's not that big of a deal, I was just curious what could be causing it. And with the Ps crashes I guess I'll just stick with Yosemite for the time being.

Have you run Disk Utility from your Yosemite Recovery partition? You may want to run Verify Disk and Verify Permissions and see if they need to be repaired. Does the mini go to a log in screen, where you select your User account and log in to it, or, does it start up and go right to your desktop? If it goes right to your desktop, then it still has to access the hdd where your users home folder is located, which is causing the bottleneck. You may want to just put all your media (files, pictures, music and videos) on the second hard drive and leave your home folder on the ssd, or get a bigger ssd.

I have ran Disk Utility and it didn't seem to help.

I tried both ways. With or without logging in and there was no difference.

To be more clear, for instance, when I choose restart from the Apple menu, holding option so I don't get the warning window, thats when the lag time starts. It sits there with the spinning indicator for awhile then the screen goes black and sleep mode starts on my monitor. Then about 20-30 more seconds I get the Chime. After the Chime it boots really quick.

This happens both on the SSD partition with the home folder and on it. And with the El Cap installed on the SSD and home folder on a HDD. Yosemite reboots and shuts down extremely fast with the SSD HDD home folder combo.

There may well be some confusion over the Home folder location. I think your solution is to save pennies for an 500GB or larger SSD. In my opinion El Capitan is much faster than Yosemite.

Thanks for the replies. I would really like a bigger SSD so I can have everything on one drive.

The thing is that I have El Cap on a partition of the SSD drive so it shouldn't be looking for the Home folder should it?

Everything else seems to work fine when booted up into El Cap other than Photoshop and some color mismatch issues but thats whole new issue lol.

Was the El Capitan on the partition a new install and did you copy things over from the HDD? I think the Home folder is the problem.

Yes. When I first upgraded months ago to El Cap I upgraded from Yosemite. Had some of the same issues that I'm having now so I cloned back Yosemite. Then a few days ago I thought I would try it again. So I downloaded El Cap and started having issues with Photoshop. So That's when I partitioned part of my SSD to troubleshoot. So as of now I have Yosemite on the SSD and Yosemite's Home folder on the HDD which I have zero problems with. It shuts down and reboots in seconds. Then, I have a partition on the SSD that only has El Cap. Nothing copied over or no Home folder moved.

When I do a cold restart, it boots up fine into El Cap. Within seconds. It's when I'm booted up into El Cap and restart or shutdown I get the circle icon for awhile then the screen sleeps for awhile then it takes up to a min to get the Chime. Then after the Chime it boots up very fast. So it seems like it's shutting things down in the background or something. After the Chime things are fine the lag comes in after I hit restart or shutdown.

Sorry for not explaining things correctly.

Like me Jake the poor thing is confused over all the Home folder business.

So, right now you have Yosemite and El Capitan installed onto the 128gb SSD. How did you divide the space for each? How much space is free for each? Where is the Home folder located? External or internal? How big is this drive? How is connected?

Photoshop is a resource hog.

Yes both are on a 128GB SSD drive that has a 30GB partition with 14GB of free space with El Cap on it for troubleshooting. Yosemite's home folder is on a 500GB 7200 internal HDD with 475GB of free space. All drives are internal.

Like I said the problem is after I hit restart or shutdown. It can take up to a min to get the Chime then after that it boots up very fast as Yosemite does.

If the SSD is in the optical drive slot, try changing them about and in System preferences > Startup Disk choose the SSD. I am curious you have two internal drives as Minis have not had an internal drive since 2010. If the SSD is actually an external SSD running via USB that would explain everything. There is nothing to be gained and a lot to be lost running an SSD from USB.

I bought the Dual Hard Drive Kit and installed it a few years ago so both drives are internal.

https://www.ifixit.com/Guide/Installing+Mac+Mini+Late+2012+Dual+Hard+Drive+Kit/11713

Just an update. I installed a Samsung 850 SSD 500GB and have everything on the drive including the home folder. I left the Samsung 128GB drive in there also and the only thing installed on it is El Cap and it still has the slow shutdown/restart. So I have no idea what it could be.

Another update. I did a clean install of Sierra and it does the same thing with the slow to get to the chime after a restart. I did notice that it will boot normally if I choose the disk from start up disk in system preferences. It's not that big of a deal but it's just one of those things I would like to know what could be causing it.

If your only problem is some slow reboot time but otherwise everything is working well, just use it and forget about some problem that probably doesn't even exist.